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Article ; Online: Rome III criteria capture higher irritable bowel syndrome SNP-heritability and highlight a novel genetic link with cardiovascular traits.

Tavares, Leticia Camargo / Lopera-Maya, Esteban Alexander / Bonfiglio, Ferdinando / Zheng, Tenghao / Sinha, Trishla / Marques, Francine Zanchetta / Zhernakova, Alexandra / Sanna, Serena / D'Amato, Mauro

Cellular and molecular gastroenterology and hepatology

2024

Abstract: Background & aims: Irritable bowel syndrome (IBS) shows genetic predisposition, and large-scale genome-wide association studies (GWAS) are emerging, based on heterogeneous disease definitions. We aimed at investigating the genetic architecture of IBS ... ...

Abstract	Background & aims: Irritable bowel syndrome (IBS) shows genetic predisposition, and large-scale genome-wide association studies (GWAS) are emerging, based on heterogeneous disease definitions. We aimed at investigating the genetic architecture of IBS defined according to gold-standard Rome Criteria. Methods: We conducted GWAS meta-analyses of Rome III IBS and its subtypes in 24,735 IBS cases and 77,149 asymptomatic controls from two independent European cohorts (UK Biobank and Lifelines). SNP-based heritability (h Results: Rome III IBS showed significant SNP-heritability (up to 13%) and similar genetic architecture across subtypes, including those with manifestations at the opposite ends of the symptom spectrum (r Conclusions: Rome III Criteria capture higher SNP-heritability than previously estimated for IBS. The identified link between IBS and cardiovascular traits may contribute to the delineation of alternative therapeutic strategies, warranting further investigation.
Language	English
Publishing date	2024-04-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	2819778-1
ISSN	2352-345X ; 2352-345X
ISSN (online)	2352-345X
ISSN	2352-345X
DOI	10.1016/j.jcmgh.2024.04.002
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Phenotypic and Genetic Factors Associated with Absence of Cardiomyopathy Symptoms in PLN:c.40_42delAGA Carriers.

Lopera-Maya, Esteban A / Li, Shuang / de Brouwer, Remco / Nolte, Ilja M / van Breen, Justin / Jongbloed, Jan D H / Swertz, Morris A / Snieder, Harold / Franke, Lude / Wijmenga, Cisca / de Boer, Rudolf A / Deelen, Patrick / van der Zwaag, Paul A / Sanna, Serena

Journal of cardiovascular translational research

2023 Volume 16, Issue 6, Page(s) 1251–1266

Abstract: The c.40_42delAGA variant in the phospholamban gene (PLN) has been associated with dilated and arrhythmogenic cardiomyopathy, with up to 70% of carriers experiencing a major cardiac event by age 70. However, there are carriers who remain asymptomatic at ... ...

Abstract	The c.40_42delAGA variant in the phospholamban gene (PLN) has been associated with dilated and arrhythmogenic cardiomyopathy, with up to 70% of carriers experiencing a major cardiac event by age 70. However, there are carriers who remain asymptomatic at older ages. To understand the mechanisms behind this incomplete penetrance, we evaluated potential phenotypic and genetic modifiers in 74 PLN:c.40_42delAGA carriers identified in 36,339 participants of the Lifelines population cohort. Asymptomatic carriers (N = 48) showed shorter QRS duration (- 5.73 ms, q value = 0.001) compared to asymptomatic non-carriers, an effect we could replicate in two different independent cohorts. Furthermore, symptomatic carriers showed a higher correlation (r
MeSH term(s)	Humans ; Aged ; Mutation ; Cardiomyopathies/diagnosis ; Cardiomyopathies/genetics ; Calcium-Binding Proteins/genetics ; Genotype
Chemical Substances	phospholamban ; Calcium-Binding Proteins
Language	English
Publishing date	2023-01-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2422411-X
ISSN	1937-5395 ; 1937-5387
ISSN (online)	1937-5395
ISSN	1937-5387
DOI	10.1007/s12265-022-10347-5
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Article ; Online: Host genetic regulation of human gut microbial structural variation.

Zhernakova, Daria V / Wang, Daoming / Liu, Lei / Andreu-Sánchez, Sergio / Zhang, Yue / Ruiz-Moreno, Angel J / Peng, Haoran / Plomp, Niels / Del Castillo-Izquierdo, Ángela / Gacesa, Ranko / Lopera-Maya, Esteban A / Temba, Godfrey S / Kullaya, Vesla I / van Leeuwen, Sander S / Xavier, Ramnik J / de Mast, Quirijn / Joosten, Leo A B / Riksen, Niels P / Rutten, Joost H W /

Netea, Mihai G / Sanna, Serena / Wijmenga, Cisca / Weersma, Rinse K / Zhernakova, Alexandra / Harmsen, Hermie J M / Fu, Jingyuan

Nature

2024 Volume 625, Issue 7996, Page(s) 813–821

Abstract: Although the impact of host genetics on gut microbial diversity and the abundance of specific taxa is well ... ...

Abstract	Although the impact of host genetics on gut microbial diversity and the abundance of specific taxa is well established
MeSH term(s)	Humans ; Acetylgalactosamine/metabolism ; Bacteria/classification ; Bacteria/genetics ; Bacteria/isolation & purification ; Cohort Studies ; Computer Simulation ; Faecalibacterium prausnitzii/genetics ; Gastrointestinal Microbiome/genetics ; Genome, Human/genetics ; Genotype ; Host Microbial Interactions/genetics ; In Vitro Techniques ; Metagenome/genetics ; Multigene Family ; Netherlands ; Tanzania
Chemical Substances	ABO protein, human (EC 2.4.1.-) ; Acetylgalactosamine (KM15WK8O5T) ; FUT2 protein, human
Language	English
Publishing date	2024-01-03
Publishing country	England
Document type	Meta-Analysis ; Journal Article
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-023-06893-w
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Article ; Online: Novel ancestry-specific primary open-angle glaucoma loci and shared biology with vascular mechanisms and cell proliferation.

Lo Faro, Valeria / Bhattacharya, Arjun / Zhou, Wei / Zhou, Dan / Wang, Ying / Läll, Kristi / Kanai, Masahiro / Lopera-Maya, Esteban / Straub, Peter / Pawar, Priyanka / Tao, Ran / Zhong, Xue / Namba, Shinichi / Sanna, Serena / Nolte, Ilja M / Okada, Yukinori / Ingold, Nathan / MacGregor, Stuart / Snieder, Harold /

Surakka, Ida / Shortt, Jonathan / Gignoux, Chris / Rafaels, Nicholas / Crooks, Kristy / Verma, Anurag / Verma, Shefali S / Guare, Lindsay / Rader, Daniel J / Willer, Cristen / Martin, Alicia R / Brantley, Milam A / Gamazon, Eric R / Jansonius, Nomdo M / Joos, Karen / Cox, Nancy J / Hirbo, Jibril

Cell reports. Medicine

2024 Volume 5, Issue 2, Page(s) 101430

Abstract: Primary open-angle glaucoma (POAG), a leading cause of irreversible blindness globally, shows disparity in prevalence and manifestations across ancestries. We perform meta-analysis across 15 biobanks (of the Global Biobank Meta-analysis Initiative) (n = ... ...

Abstract	Primary open-angle glaucoma (POAG), a leading cause of irreversible blindness globally, shows disparity in prevalence and manifestations across ancestries. We perform meta-analysis across 15 biobanks (of the Global Biobank Meta-analysis Initiative) (n = 1,487,441: cases = 26,848) and merge with previous multi-ancestry studies, with the combined dataset representing the largest and most diverse POAG study to date (n = 1,478,037: cases = 46,325) and identify 17 novel significant loci, 5 of which were ancestry specific. Gene-enrichment and transcriptome-wide association analyses implicate vascular and cancer genes, a fifth of which are primary ciliary related. We perform an extensive statistical analysis of SIX6 and CDKN2B-AS1 loci in human GTEx data and across large electronic health records showing interaction between SIX6 gene and causal variants in the chr9p21.3 locus, with expression effect on CDKN2A/B. Our results suggest that some POAG risk variants may be ancestry specific, sex specific, or both, and support the contribution of genes involved in programmed cell death in POAG pathogenesis.
MeSH term(s)	Male ; Female ; Humans ; Genetic Predisposition to Disease/genetics ; Glaucoma, Open-Angle/genetics ; Glaucoma, Open-Angle/epidemiology ; Polymorphism, Single Nucleotide ; Cell Proliferation ; Biology
Language	English
Publishing date	2024-02-20
Publishing country	United States
Document type	Meta-Analysis ; Journal Article
ISSN	2666-3791
ISSN (online)	2666-3791
DOI	10.1016/j.xcrm.2024.101430
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Article ; Online: Author Correction: Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project.

Nature genetics

2022 Volume 54, Issue 9, Page(s) 1448

Language	English
Publishing date	2022-07-20
Publishing country	United States
Document type	Published Erratum
ZDB-ID	1108734-1
ISSN	1546-1718 ; 1061-4036
ISSN (online)	1546-1718
ISSN	1061-4036
DOI	10.1038/s41588-022-01164-2
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Zs.A 3613: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article: Lack of Association Between Genetic Variants at

Lopera Maya, Esteban A / van der Graaf, Adriaan / Lanting, Pauline / van der Geest, Marije / Fu, Jingyuan / Swertz, Morris / Franke, Lude / Wijmenga, Cisca / Deelen, Patrick / Zhernakova, Alexandra / Sanna, Serena

Frontiers in genetics

2020 Volume 11, Page(s) 613

Abstract: Coronavirus disease 2019 (COVID-19) shows a wide variation in expression and severity of symptoms, from very mild or no symptoms, to flu-like symptoms, and in more severe cases, to pneumonia, acute respiratory distress syndrome, and even death. Large ... ...

Abstract	Coronavirus disease 2019 (COVID-19) shows a wide variation in expression and severity of symptoms, from very mild or no symptoms, to flu-like symptoms, and in more severe cases, to pneumonia, acute respiratory distress syndrome, and even death. Large differences in outcome have also been observed between males and females. The causes for this variability are likely to be multifactorial, and to include genetics. The SARS-CoV-2 virus responsible for the infection depends on two human genes: the human receptor angiotensin converting enzyme 2 (
Keywords	covid19
Language	English
Publishing date	2020-06-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2020.00613
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Article ; Online: Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project.

Nature genetics

2022 Volume 54, Issue 2, Page(s) 143–151

Abstract: Host genetics are known to influence the gut microbiome, yet their role remains poorly understood. To robustly characterize these effects, we performed a genome-wide association study of 207 taxa and 205 pathways representing microbial composition and ... ...

Abstract	Host genetics are known to influence the gut microbiome, yet their role remains poorly understood. To robustly characterize these effects, we performed a genome-wide association study of 207 taxa and 205 pathways representing microbial composition and function in 7,738 participants of the Dutch Microbiome Project. Two robust, study-wide significant (P < 1.89 × 10
MeSH term(s)	ABO Blood-Group System/genetics ; Bacterial Physiological Phenomena ; Bifidobacterium/physiology ; Diet ; Fucosyltransferases/genetics ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Genetic Variation ; Genome, Human ; Genome-Wide Association Study ; Host Microbial Interactions ; Humans ; Lactase/genetics ; Metabolic Networks and Pathways ; Metagenome ; Multifactorial Inheritance ; Netherlands ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Sodium Chloride, Dietary ; Triglycerides/blood ; Galactoside 2-alpha-L-fucosyltransferase
Chemical Substances	ABO Blood-Group System ; Sodium Chloride, Dietary ; Triglycerides ; Fucosyltransferases (EC 2.4.1.-) ; Lactase (EC 3.2.1.108)
Language	English
Publishing date	2022-02-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1108734-1
ISSN	1546-1718 ; 1061-4036
ISSN (online)	1546-1718
ISSN	1061-4036
DOI	10.1038/s41588-021-00992-y
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Article ; Online: Lack of Association Between Genetic Variants at ACE2 and TMPRSS2 Genes Involved in SARS-CoV-2 Infection and Human Quantitative Phenotypes

Lopera Maya, Esteban A. / van der Graaf, Adriaan / Lanting, Pauline / van der Geest, Marije / Fu, Jingyuan / Swertz, Morris / Franke, Lude / Wijmenga, Cisca / Deelen, Patrick / Zhernakova, Alexandra / Sanna, Serena

Frontiers in Genetics

2020 Volume 11

Keywords	Genetics(clinical) ; Molecular Medicine ; Genetics ; covid19
Publisher	Frontiers Media SA
Publishing country	ch
Document type	Article ; Online
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2020.00613
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Article ; Online: Lack of Association Between Genetic Variants at ACE2 and TMPRSS2 Genes Involved in SARS-CoV-2 Infection and Human Quantitative Phenotypes

Esteban A. Lopera Maya / Adriaan van der Graaf / Pauline Lanting / Marije van der Geest / Jingyuan Fu / Morris Swertz / Lude Franke / Cisca Wijmenga / Patrick Deelen / Alexandra Zhernakova / Serena Sanna / Lifelines Cohort Study

Frontiers in Genetics, Vol

2020 Volume 11

Abstract	Coronavirus disease 2019 (COVID-19) shows a wide variation in expression and severity of symptoms, from very mild or no symptoms, to flu-like symptoms, and in more severe cases, to pneumonia, acute respiratory distress syndrome, and even death. Large differences in outcome have also been observed between males and females. The causes for this variability are likely to be multifactorial, and to include genetics. The SARS-CoV-2 virus responsible for the infection depends on two human genes: the human receptor angiotensin converting enzyme 2 (ACE2) for cell invasion, and the serine protease TMPRSS2 for S protein priming. Genetic variation in these two genes may thus modulate an individual's genetic predisposition to infection and virus clearance. While genetic data on COVID-19 patients is being gathered, we carried out a phenome-wide association scan (PheWAS) to investigate the role of these genes in other human phenotypes in the general population. We examined 178 quantitative phenotypes including cytokines and cardio-metabolic biomarkers, as well as usage of 58 medications in 36,339 volunteers from the Lifelines population cohort, in relation to 1,273 genetic variants located in or near ACE2 and TMPRSS2. While none reached our threshold for significance, we observed several interesting suggestive associations. For example, single nucleotide polymorphisms (SNPs) near the TMPRSS2 genes were associated with thrombocytes count (p = 1.8 × 10−5). SNPs within the ACE2 gene were associated with (1) the use of angiotensin II receptor blockers (ARBs) combination therapies (p = 5.7 × 10−4), an association that is significantly stronger in females (pdiff = 0.01), and (2) with the use of non-steroid anti-inflammatory and antirheumatic products (p = 5.5 × 10−4). While these associations need to be confirmed in larger sample sizes, they suggest that these variants could play a role in diseases such as thrombocytopenia, hypertension, and chronic inflammation that are often observed in the more severe COVID-19 cases. Further investigation of these genetic variants in the context of COVID-19 is thus promising for better understanding of disease variability. Full results are available at https://covid19research.nl.
Keywords	PheWAS ; ACE2 ; TMPRSS2 ; NSAIDs (non-steroidal anti-inflammatory drugs) ; ARBs (angiotensin II receptor blockers) ; COVID-19 ; Genetics ; QH426-470 ; covid19
Subject code	616
Language	English
Publishing date	2020-06-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Table_2_Lack of Association Between Genetic Variants at ACE2 and TMPRSS2 Genes Involved in SARS-CoV-2 Infection and Human Quantitative Phenotypes.XLSX

2020

Abstract	Coronavirus disease 2019 (COVID-19) shows a wide variation in expression and severity of symptoms, from very mild or no symptoms, to flu-like symptoms, and in more severe cases, to pneumonia, acute respiratory distress syndrome, and even death. Large differences in outcome have also been observed between males and females. The causes for this variability are likely to be multifactorial, and to include genetics. The SARS-CoV-2 virus responsible for the infection depends on two human genes: the human receptor angiotensin converting enzyme 2 (ACE2) for cell invasion, and the serine protease TMPRSS2 for S protein priming. Genetic variation in these two genes may thus modulate an individual's genetic predisposition to infection and virus clearance. While genetic data on COVID-19 patients is being gathered, we carried out a phenome-wide association scan (PheWAS) to investigate the role of these genes in other human phenotypes in the general population. We examined 178 quantitative phenotypes including cytokines and cardio-metabolic biomarkers, as well as usage of 58 medications in 36,339 volunteers from the Lifelines population cohort, in relation to 1,273 genetic variants located in or near ACE2 and TMPRSS2. While none reached our threshold for significance, we observed several interesting suggestive associations. For example, single nucleotide polymorphisms (SNPs) near the TMPRSS2 genes were associated with thrombocytes count (p = 1.8 × 10 −5 ). SNPs within the ACE2 gene were associated with (1) the use of angiotensin II receptor blockers (ARBs) combination therapies (p = 5.7 × 10 −4 ), an association that is significantly stronger in females (p dif f = 0.01), and (2) with the use of non-steroid anti-inflammatory and antirheumatic products (p = 5.5 × 10 −4 ). While these associations need to be confirmed in larger sample sizes, they suggest that these variants could play a role in diseases such as thrombocytopenia, hypertension, and chronic inflammation that are often observed in the more severe COVID-19 cases. Further investigation of these genetic variants in the context of COVID-19 is thus promising for better understanding of disease variability. Full results are available at https://covid19research.nl.
Keywords	Genetics ; Genetic Engineering ; Biomarkers ; Developmental Genetics (incl. Sex Determination) ; Epigenetics (incl. Genome Methylation and Epigenomics) ; Gene Expression (incl. Microarray and other genome-wide approaches) ; Genome Structure and Regulation ; Genomics ; Genetically Modified Animals ; Livestock Cloning ; Gene and Molecular Therapy ; PheWAS ; ACE2 ; TMPRSS2 ; NSAIDs (non-steroidal anti-inflammatory drugs) ; ARBs (angiotensin II receptor blockers) ; COVID-19 ; SARS-CoV-2 ; covid19
Subject code	572
Publishing date	2020-06-08T14:39:08Z
Publishing country	uk
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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